you can rule out bushings, DC/DCC issues, or bad motor. That leaves you with uneven flywheels, rubbing flywheels, vibrating mech in the trucks.
This is clearly caused by vibrations in the rotating assy that is magnified or perpetuated by the body shell. you are going to just have to examine the mechanics of the engine until you find out what it is. Here are some tips.
1. Remove the drivelines from both sides of the motor and trucks. Put shell back on and see if the sound is there. If yes then motor/flywheels are the issue. If no then they are good move to step 2.
2. Install one driveline only (front or rear does not matter) run engine with shell on and see if the sound returns. If yes check out that truck or driveline. If no, repeat step with other side, one drive line only. Also even if the sound is there try the other truck anyway just in case it makes noise too.
If the gears are making the noise you can try to polish the gears with some toothpaste. Yes I said toothpaste, it has mild abrasives that will help run the gears in. clean the oil off the gears and then relube them with an ample amount of toothpaste and run the train about 1/2 to 3/4 thottle, no cars for about 30-40 minutes. Clean the tooth paste off and reoil the gears and reassemble.